MolNFT v1 · #67343 · protein
Covalent ubiquitin-USP5 complex
3IHP · Ubiquitin carboxyl-terminal hydrolase 5: “Covalent ubiquitin-USP5 complex”. X-ray diffraction, 3 ligands (NEH, ZN, CL), 16 pockets (best druggability 0.72). MolNFT v1 #67343 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3IHP
- Type
- protein
- Length
- 1,504 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 5; Ubiquitin
- EC
- 3.1.2.15
- UniProt
- P62988
- Ligands
- NEH, ZN, CL
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) | protein | 673 | 33% helix, 22% strand | — |
| B | Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) | protein | 681 | 32% helix, 21% strand | — |
| C, D | Ubiquitin | protein | 75 | 20% helix, 29% strand | P62988 |
Ligands and binding sites
- NEH · Ethanamine · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.72 | 0.83 | 41 | empty |
| 2 | 400 | 0.70 | 0.82 | 37 | empty |
| 3 | 700 | 0.68 | 0.76 | 78 | empty |
| 4 | 456 | 0.64 | 0.77 | 42 | empty |
| 5 | 130 | 0.61 | 0.86 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2265 Ų buried · 45 hydrogen bonds · protein-protein
- B–D · 2235 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 439 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 3IHP · Covalent Ubiquitin-Usp5 Complex · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 3IHP · PDBe 3IHP · UniProt P62988
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